Structure of antiamoebin I from high resolution field desorption and gas chromatographic mass spectrometry studies

Isolation, Characterization, and Bioherbicidal Potential of the 16-Residue Peptaibols from Emericellopsis sp. XJ1056

Eco-friendly bioherbicides are urgently needed for managing the problematic weed Amaranthus retroflexus. A mass spectrometry- and bioassay-guided screening approach was employed to identify phytotoxic secondary metabolites from fungi for the development of such bioherbicides. This effort led to the discovery of six phytotoxic 16-residue peptaibols, including five new compounds (2-6) and a known congener (1), from Emericellopsis sp. XJ1056. Their planar structures were elucidated through the analysis of tandem mass and NMR spectroscopic data. The absolute configurations of the chiral amino acids were determined by advanced Marfey's method and chiral-phase liquid chromatography-mass spectrometry (LC-MS) analysis. Bioinformatic analysis and targeted gene disruption identified the biosynthetic gene cluster for these peptaibols. Compounds 1 and 2 significantly inhibited the radicle growth of A. retroflexus seedlings, and 1 demonstrated potent postemergence herbicidal activity against A. retroflexus while exhibiting minimal toxicity to Sorghum bicolor. Structure-activity relationship analysis underscored the importance of trans-4-hydroxy-l-prolines at both the 10th and 13th positions for the herbicidal activities of these peptaibols.

Helical Antimicrobial Peptide Foldamers Containing Non-proteinogenic Amino Acids

Antimicrobial peptides (AMPs) are potential novel therapeutic drugs against microbial infections. Most AMPs function by disrupting microbial membranes because of their amphipathic properties and ordered secondary structures. In this minireview, we describe recent efforts to develop helical AMP foldamers containing non-proteinogenic amino acids, such as α,α-disubstituted α-amino acids, β-amino acids, γ-amino acids, side-chain stapling and N-alkyl glycines.

NP/MS since 1970: from the basement to the bench top

This Highlight explores the evolution of applications of mass spectrometric technologies in the context of natural products research since the 1970's. The central themes are the analysis of mixtures, dereplication (identification) and structure determination. The ascension of HPLC as the method of choice for the analysis of pharmaceuticals was a driving force for the development of interfaces for coupling of HPLC and MS. An example of sequential analysis of fragment ions or MS/MS or MS(n) methods to provide detailed structural information on muraymycins, a family of uridyl-peptide antibiotics, is presented.

Molecular dynamics simulation of the antiamoebin ion channel: linking structure and conductance

Molecular-dynamics simulations were carried out to ascertain which of the potential multimeric forms of the transmembrane peptaibol channel, antiamoebin, is consistent with its measured conductance. Estimates of the conductance obtained through counting ions that cross the channel and by solving the Nernst-Planck equation yield consistent results, indicating that the motion of ions inside the channel can be satisfactorily described as diffusive. The calculated conductance of octameric channels is markedly higher than the conductance measured in single channel recordings, whereas the tetramer appears to be nonconducting. The conductance of the hexamer was estimated to be 115 ± 34 pS and 74 ± 20 pS, at 150 mV and 75 mV, respectively, in satisfactory agreement with the value of 90 pS measured at 75 mV. On this basis, we propose that the antiamoebin channel consists of six monomers. Its pore is large enough to accommodate K⁺ and Cl⁻ with their first solvation shells intact. The free energy barrier encountered by K⁺ is only 2.2 kcal/mol whereas Cl⁻ encounters a substantially higher barrier of nearly 5 kcal/mol. This difference makes the channel selective for cations. Ion crossing events are shown to be uncorrelated and follow Poisson statistics.

Antimicrobial peptaibols, novel suppressors of tumor cells, targeted calcium-mediated apoptosis and autophagy in human hepatocellular carcinoma cells

Background

Hepatocellular carcinoma (HCC) is one of the most common cancers in the world which is highly chemoresistant to currently available chemotherapeutic agents. Thus, novel therapeutic targets are needed to be sought for the successful treatment of HCC. Peptaibols, a family of peptides synthesized non-ribosomally by the Trichoderma species and other fungi, exhibit antibiotic activities against bacteria and fungi. Few studies recently showed that peptaibols exerted cytotoxicity toward human lung epithelial and breast carcinoma cells. However, the mechanism involved in peptaibol-induced cell death remains poorly understood.

Results

Here, we showed that Trichokonin VI (TK VI), a peptaibol from Trichoderma pseudokoningii SMF2, induced growth inhibition of HCC cells in a dose-dependent manner. It did not obviously impair the viability of normal liver cells at lower concentration. Moreover, the suppression of cell viability resulted from the programmed cell death (PCD) with characteristics of apoptosis and autophagy. An influx of Ca²⁺ triggered the activation of μ-calpain and proceeded to the translocation of Bax to mitochondria and subsequent promotion of apoptosis. On the other hand, typically morphological characteristics consistent with autophagy were also observed by punctate distribution of MDC staining and the induction of LC3-II, including extensive autophagic vacuolization and enclosure of cell organelles by these autophagosomes. More significantly, specific depletion of Bak expression by small RNA interfering (siRNA) could partly attenuate TK VI-induced autophagy. However, siRNA against Bax led to increased autophagy.

Conclusion

Taken together, these findings showed for the first time that peptaibols were novel regulators involved in both apoptosis and autophagy, suggesting that the class of peptaibols might serve as potential suppressors of tumor cells.

Trichogin: a paradigm for lipopeptaibols

Lipopeptaibols are members of a novel family of naturally occurring, short peptides with antimicrobial activity, characterized by a lipophilic acyl chain at the N-terminus, a high content of turn/helix inducing alpha-aminoisobutyric acid and a 1,2-amino alcohol at the C-terminus. Using solution methods, the prototypical lipopeptaibol trichogin GA IV and a large series of appropriately designed analogues were synthesized, which allow: (i) determination of the minimal lipid chain and peptide main-chain lengths for the onset of membrane activity, and (ii) exploitation of a number of physico-chemical techniques aimed at assessing the trichogin preferred conformation under a variety of conditions and at investigating its mechanism of interaction with the phospholipid membranes.

The occurrence of peptaibols and structurally related peptaibiotics in fungi and their mass spectrometric identification via diagnostic fragment ions

Peptaibols and related peptide antibiotics (peptaibiotics) display diagnostically useful fragmentation patterns during mass spectrometry (FAB-MS, ESI-CID-MS/MS and CID-MSn]. The paper compiles fragmentation data of pseudo-molecular ions reported in the literature as a guide to the rational identification of recurrently isolated and new peptaibols and peptaibiotics. Taxonomic and ecological aspects of microorganisms producing peptaibols and peptaibiotics are discussed.

Solution NMR studies of antiamoebin, a membrane channel-forming polypeptide

Antiamoebin I is a membrane-active peptaibol produced by fungi of the species Emericellopsis which is capable of forming ion channels in membranes. Previous structure determinations by x-ray crystallography have shown the molecule is mostly helical, with a deep bend in the center of the polypeptide, and that the backbone structure is independent of the solvent used for crystallization. In this study, the solution structure of antiamoebin was determined by NMR spectroscopy in methanol, a solvent from which one of the crystal structures was determined. The ensemble of structures produced exhibit a right-handed helical C terminus and a left-handed helical conformation toward the N-terminus, in contrast to the completely right-handed helices found in the crystal structures. The NMR results also suggest that a "hinge" region exists, which gives flexibility to the polypeptide in the central region, and which could have functional implications for the membrane insertion process. A model for the membrane insertion and assembly process is proposed based on the antiamoebin solution and crystal structures, and is contrasted with the assembly and insertion mechanism proposed for other ion channel-forming polypeptides.

Spermidine as a potential biosynthetic precursor to the 1,5-diazabicyclo[4:3:o]nonene residue in the efrapeptins

Efrapeptins are a group of microheterogeneous polypeptide antibiotics produced by the fungus Tolypocladium niveum, which are potent inhibitors of mitochondrial F1-ATPase. Efrapeptins contain an unusual 1,5-diazabicyclo[4:3:0]nonene (DBN) residue at the C-terminus. This study is driven by the hypothesis that the DBN residue could, in principle, arise by oxidative cyclization of a spermidine moiety. Electrospray ionization mass spectrometry of the peptide antibiotics 'elvapeptins' from T niveum establishes the presence of a C-terminal spermidine residue. Conversion of elvapeptins to efrapeptins by CuCl/pyridine demonstrates the transformation of the spermidine residue to the 1,5-diazabicyclo[4:3:0]nonene system by oxidative cyclization.

Structure and conformational behavior of biopolymers by density functional calculations employing periodic boundary conditions. I. The case of polyglycine, polyalanine, and poly-alpha-aminoisobutyric acid in vacuo

Fully quantum mechanical calculations exploiting periodic boundary conditions (PBC) have been applied to the study of four different regular structures (alpha- and 3(10)-helix, fully extended and repeated gamma-turns) of the infinite polypeptides of glycine, alanine, and alpha-aminoisobutyric acid (Aib) in vacuo. alpha-Helix is predicted to be the most stable conformer for polyalanine and polyglycine, being stabilized over the 3(10)-helix mainly by more favorable dipole-dipole interactions. Contrary to previous suggestions, steric effects and hydrogen-bond strengths are comparable for both helix structures. 3(10)-Helix is preferred for poly-Aib, since in this case alpha-helix is strongly distorted due to unfavorable intrachain repulsions. Extended structures and repeated gamma-turns are much less stable than helix structures for all of the polypeptides examined, mainly due to the absence of favorable long-range interactions. The optimized geometries are in good agreement with the available experimental data and reveal a remarkable dependence on the nature of the residue forming the polypeptides; at the same time the electronic and structural parameters of each residue strongly depend on the secondary structure of the polypeptides.

New sequences and new fungal producers of peptaibol antibiotics antiamoebins

Mixtures of the microheterogeneous 16-mer peptaibol antibiotics called antiamoebins (AAM) have been isolated from the culture broths of strains of the filamentous fungi Stilbella erythrocephala ATCC 28144, Stilbella fimetaria CBS 548.84 and Gliocladium catenulatum CBS 511.66. Sequences were determined using on-line HPLC together with positive- and negative-ion electrospray ionization mass spectrometry. Some characteristic features are recognized in the mass spectrometric fragmentation pattern of AAM. From a sample originally used for sequencing AAM (from Hindustan Antibiotics, Ltd., Pimpri, Poona-411018, India), and a sample of AAM commercially available (from Sigma Chemicals, St. Louis, MO, USA) HPLC elution profiles and sequences were assigned. Further, sequences of AAM previously isolated from Emericellopsis synnematicola CBS 176.60 and Emericellopsis salmosynnemata CBS 382.62 were determined. The peptide designated AAM I was the most abundant in all isolates and its structure could be confirmed. AAM II was detectable as a minor component (1.9%) only in the original sample of AAM, but not in the other isolates. The structures of AAM III, IV and V, which had previously been partly assigned, were definitely established, and the new sequences AAM VI-XVI were elucidated. AAM showing Phe1/Leu1 or Phe1/Val1 exchange, respectively, are produced in amounts only by S. erythrocephala. Sequences, HPLC elution profiles ('fingerprints') and relative amounts of peptides of all isolates were correlated.

Structures of trichovirins II, peptaibol antibiotics from the mold Trichoderma viride NRRL 5243

From the culture broth of the mold Trichoderma viride NRRL 5243 a mixture of polypeptides, named trichovirins (TV), could be isolated and purified by chromatography on XAD-2 adsorber resin and Sephadex LH-20 gel. Chromatography on silica gel using chloroform/methanol 8:2 as eluent provided a mixture of peptides named TV I. Subsequent elution with chloroform/methanol 1:1 yielded a second group of peptides named TV II. That group could be separated into individual components by repetitive HPLC on an octadecylsilyl and a fluorocarbon stationary phase. The sequences of 12 peptides of TV II could be determined by electrospray ionization tandem mass spectrometry of isolated peptides and gas chromatography-mass spectrometry of methanolysates. The N-termini of the 18-mer peptides are acetylated and the C-termini consist of leucinol. Owing to the presence of alpha-aminoisobutyric acid (Aib) residues and the bactericidal and hemolytic activity, the peptides belong to the family of peptaibol antibiotics.

Isolation and sequence analysis of new peptaibol, boletusin, from Boletus spp

A new peptaibol, boletusin, was isolated from the methanol extract of the fruiting body of the mushroom, Boletus spp. Sequential determination by positive FAB MS/MS showed that boletusin is a peptide consisting of 19 amino acids, with one acetylated N-terminus residue, phenylalanine, and a C-terminal amino alcohol, tryptophanol. This peptide showed antimicrobial activity against several Gram-positive bacteria.

Antiamoebin can function as a carrier or as a pore-forming peptaibol

Antiamoebin is a 16-residue polypeptide whose crystal structure and lytic activity in membrane vesicles have recently been reported. It is a bent helical molecule and a member of the peptaibol family of antibiotics. Under conditions which produce voltage-dependent conductance activity by other members of the family, no single-channel conductance was detected for antiamoebin, and a carrier-like mechanism was put forward to account for its mode of action. We now present evidence for pore formation that is largely voltage-insensitive, with large amplitude single-channel events on top of a background conductance that may account for the previously proposed carrier-like activity. Thus, antiamoebin may be the first instance of a peptide which can function both as an ion carrier and a pore former.

The crystal state conformation of Aib-rich segments of peptaibol antibiotics

Ac-(Aib-Ala)3-OH (a protected segment of the peptaibols gliodeliquescin and paracelsin), Z-Leu-Aib-Val-Aib-Gly-OtBu (a segment of [Leu]7-gliodeliquescin), Z-Val-Aib-Aib-Gln-OtBu (a common segment of alamethicin, paracelsin, and hypelcin), and Ac-Aib-Pro-(Aib-Ala)2-OMe and Z-Aib-Pro-(Aib-Ala)2-OMe, which represent differently N(alpha)-protected 1-6 segments of alamethicin and hypelcin, have been synthesized by solution methods. The crystal-state conformations of these five Aib-containing peptides have been determined by X-ray diffraction analysis. We have confirmed that the 3(10)-helical structure is preferentially adopted by Aib-rich short peptides. An experimentally unambiguous proof for the 3(10)-->alpha-helix conversion has been provided by the two differently N-blocked -Aib-Pro-(Aib-Ala)2-OMe hexapeptides. The beta-bend ribbon conformation, commonly observed in the (Aib-Pro)n sequential oligopeptides, is not found in the -Aib-Pro-Aib-Ala-Aib-Ala-sequence. As expected on the basis of the L-configuration of the C(alpha)-monoalkylated residues, a right-handed helix screw sense was found in all peptides investigated.

The structure and function of antiamoebin I, a proline-rich membrane-active polypeptide

BACKGROUND

Antiamoebin is a member of the peptaibol family of polypeptides and has a unique antibiotic activity: it acts as an antiamoebic agent, but does not effectively haemolyze erythrocytes even though it does exhibit membrane-modifying activity.

RESULTS

The structure of antiamoebin I has been determined by X-ray crystallography at 1.4 A resolution. The molecule forms a helical structure, which, as a result of the presence of a number of proline and hydroxyproline residues, has a deep bend in the middle. Circular dichroism spectroscopy, single-channel conductance studies and fluorescence diffusion studies suggest a mode of ion transport that is entirely different from that of the other two members of the peptaibol family (alamethicin and zervamicin) whose structures and functions have been examined in detail.

CONCLUSIONS

The structure of the polypeptide has been determined and a functional model for its mode of action in membranes is presented. Although under some conditions antiamoebin may form ion channels, unlike the closely related alamethicin and zervamicin polypeptides, its major membrane-modifying activity appears to be as an ion carrier.

Crystal structure of the channel-forming polypeptide antiamoebin in a membrane-mimetic environment

Crystals of an ion-channel-forming peptaibol peptide in a partial membrane environment have been obtained by cocrystallizing antiamoebin with n-octanol. The antiamoebin molecule has a bent helical conformation very similar to that established for Leu-zervamicin, despite a significantly different sequence for residues 1-8. The bent helices assemble to form a polar channel in the shape of an hour glass that is quite comparable to that of Leu-zervamicin. The molecules of cocrystallized octanol are found in two different areas with respect to the assembly of peptide molecules. One octanol molecule mimics a membrane segment along the hydrophobic exterior of the channel assembly. The other octanol molecules fill the channel in such a way that their OH termini satisfy the C==O moieties directed into the interior of the channel. Structure parameters for C82 H27 N17 O20(.3) C8H18O are space group P2(1) 2(1) 2(1), a = 9.143(2) A, b = 28.590(8) A, c = 44.289(8) A, Z = 4, agreement factor R1 = 11.95% for 4,113 observed reflections [>4sigma(F)], resolution approximately 1.0 A.

Crystal structure of a dipeptide Boc-Aib-Phe-OMe

In order to understand the effect of the restrictions posed by the Aib residue on peptide conformation we studied the crystal structure of a dipeptide tBoc-Aib-Phe-OMe. Crystals of this compound are triclinic, space group P1 with a = 9.600(1) A, b = 10.262(1) A, c = 10.799(1) A, alpha = 98.43 degrees (1), beta = 99.18 degrees (1), gamma = 98.87 degrees (1), V = 1021.69(18) A3 and Z = 2. The structure was solved by direct methods and refined to an R-factor of 4.98%. The backbone conformational angles for the Aib residue in molecule A are in the left-handed helical region, while in molecule B they are in the right-handed helical region. The Phe residue in molecule A is in the right-handed helical conformation, while in molecule B it is in the beta-region. The peptide units are trans and show significant deviation from planarity [(omega 1 = 166.67(5) degrees and omega 2 = -177.9(5)].

Structural elucidation of XR586, a peptaibol-like antibiotic from Acremonium persicinum

A novel peptide, XR586, has been isolated from fermentations of Acremonium persicinum (Xenova culture collection number X21488). The structure of XR586 has been elucidated by means of NMR spectroscopy, electrospray and fast-atom bombardment MS, derivatization and enzymic digestion. It has been shown to be helical by CD measurements. XR586 shows many structural and conformational features in common with peptaibols, particularly the zervamicins. Peptaibol antibiotics are peptides, typically of 15-20 residues, containing a large proportion of alpha-aminoisobutyric acid (Aib) residues. These peptides adopt a helical conformation in solution and display anti-bacterial and toxic properties due to their ability to form pores in membranes. However, while XR586 contains several Aib residues, it lacks a terminal phenylalaninol and terminates in the sequence Phe-Gly. The lack of reduction of the penultimate residue at the C-terminus may indicate that this step is normally at the end of the biosynthetic pathway of peptaibols and occurs with cleavage of Gly. The 1H chemical shift assignments of XR586 are reported in Supplementary Publication SUP 50179 (3 pages), which has been deposited at the British Library Document Supply Centre, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1996) 313, 9 ("Deposition of data').

Structure determination of racemic trichogin A IV using centrosymmetric crystals

Direct methods of crystal structure solution are greatly facilitated in centrosymmetric space groups where the complexity of the phase-problem is reduced. For most peptides and proteins, crystallization in a centrosymmetric arrangement is precluded by an intrinsic dissymmetry due to the constituent chiral amino acid residues. The synthetic accessibility of peptide sequences containing amino acids of either chirality offers the possibility for co-crystallization of racemic crystals. We report here the first use of such an approach for the de novo structure determination of a medium-sized molecule, trichogin A IV, which is a constituent of a fungal lipopeptaibol mixture possessing membrane-modifying properties of biological interest.

Purification and Characterization of an l -Amino Amidase from Mycobacterium neoaurum ATCC 25795

An l -amino amidase from Mycobacterium neoaurum ATCC 25795 responsible for the enantioselective resolution of dl -α-methyl valine amide was purified and characterized. The purification procedure included ammonium sulfate fractionation, gel filtration, and anion-exchange chromatography, which resulted in a homogeneous preparation of the enzyme with a native molecular mass of 136 kDa and a subunit molecular mass of 40 kDa. The purified enzyme displayed the highest activity at 50°C and at pH 8.0 and 9.5. The enzyme was strongly inhibited by the metal-chelating agent 1,10-phenanthroline, the disulfide-reducing agent dithiothreitol, and the cysteine proteinase inhibitor iodoacetamide. The purified amino amidase showed a unique l -enantioselective activity towards a broad range of both α-H- and α-alkyl-substituted amino acid amides, with the highest activity towards the cyclic amino acid amide dl -proline amide. No activity was measured with dl -mandelic acid amide nor with the dipeptide l -phenylalanine- l -leucine. The highest catalytic efficiency ( k cat / K m ratio) was measured with dl -α-allyl alanine amide, dl -α-methyl phenylalanine amide, and dl -α-methyl leucine amide.

Sequence and solution conformation of the 20-residue peptaibols, saturnisporins SA II and SA IV

Saturnisporins SA II and SA IV are the major components of the 20-residue peptaibol mixture isolated from a culture of the fungus Trichoderma saturnisporum. These peptides exhibit antibiotic activity against Staphylococcus aureus. Their sequences were derived from unequivocal methodology implying the combined use of positive ion FAB mass spectrometry and NMR: the majority of the sequences result from mass spectrometry fragmentations and the location of isomeric residues arises either from analysis of ROESY cross-peaks between contiguous amide protons or from heteronuclear 2J or 3J 1H-13C couplings detected in long-range 1H-13C COSY experiments. The sequence specific 1H and 13C NMR assignments are described. Saturnisporins SA II and SA IV exhibit similar secondary structures, as deduced from their ROESY patterns and 3JNHC alpha H coupling constant values, together with amide hydrogen-deuterium exchange rates and temperature coefficients of amide and carbonyl groups. An overall alpha-helical structure is proposed, maintaining two regions of distortion to this regular structure; i) the N-terminal part, which contains 3(10) and mixed alpha-3(10) turns, and ii) the Aib10-Val15 region, including a Pro residue which accommodates a bend stabilized by two 3(10) H-bonds.